Biology subjects

Hanif, S.

Publications and source records attributed to Hanif, S..

7 recordsLinked to original sources

bioRxiv2025

Dirt floors and domestic animals are associated with soilborne exposure to antimicrobial resistant E. coli in rural Bangladeshi households

Soil can harbor enteropathogens and antimicrobial-resistant organisms in settings with domestic animals. We enrolled 49 households with young children (28 soil floors, 21 concrete floors) in Bangladesh and recorded animal ownership/management. Staff swabbed the floor of childrens sleeping area with a sterile sponge and collected floor dust and a child hand rinse. We used IDEXX QuantiTray/2000 with and without cefotaxime supplementation to enumerate cefotaxime-resistant and generic E. coli. There was 8.0 g/m2 of dust on soil floors vs. 0.2 g/m2 on concrete floors (p-value=0.005). We detected E. coli on 100% of soil vs. 86% of concrete floors and cefotaxime-resistant E. coli on 89% of soil vs. 43% of concrete floors (p-values<0.05). Cefotaxime-resistant E. coli prevalence on floors was 36% in compounds without animals, 79% in compounds with animals and 100% if animals stayed indoors overnight or the floor had animal feces; associations were strongest for chickens. In multivariable models, generic and cefotaxime-resistant E. coli counts were 1.5-2 log higher on soil vs. concrete floors, and counts on floors and child hands were 0.17-0.24 log higher for every 10 additional chickens owned (p-values<0.05). Efforts to mitigate infections and antimicrobial resistance in low-income countries should test flooring improvements and hygienic animal management. SynopsisIn rural Bangladeshi households, generic and cefotaxime-resistant E. coli were more common on soil floors than concrete floors and among households with higher cohabitation intensity with domestic animals, especially chickens.

microbiology↗

bioRxiv2025

Investigating Cement-Based Surfaces as a Sustainable Flooring Solution to Improve Ascaris Egg Removal and Inactivation in Low-Resource Settings

Soil-transmitted helminths, like Ascaris, are significant contributors to disease burden in low- and middle-income countries (LMICs). Infections are associated with growth faltering and mortality in children and are often transmitted through contact with eggs in fecally contaminated soil. Interventions, like replacing household soil floors with cement-based alternatives, may reduce exposure to Ascaris eggs, but there are currently no estimates on the removal or survival of Ascaris eggs on cement-based surfaces. This study addresses that knowledge gap by evaluating the removal of Ascaris eggs from mopping and the survival of Ascaris eggs on two cement-based mixes: an Ordinary Portland Cement (OPC) mortar and an OPC mortar with fly ash, which provides a more sustainable alternative to the OPC mortar mix. We assessed egg survival at two temperatures representing the dry (15{degrees}C) and wet (34{degrees}C) seasons in Bangladesh using two different egg enumeration methods. After mopping, over 92% of viable eggs were removed from surfaces, with no significant differences between cement-based mixes (p = 0.51). The first-order decay rate constants (k) of Ascaris eggs were similar between mix designs (p = 0.62) but varied significantly between temperatures (p = 4.2 x 10-25) and egg enumeration methods (p = 2.4 x 10-8). The k values were of greater magnitude at 34{degrees}C compared to at 15{degrees}C. At 15{degrees}C, k values were not significantly different from zero, indicating no inactivation. The k values we obtained were comparable to those reported in previous studies for different matrices, indicating comparable inactivation of Ascaris eggs on cement-based surfaces compared to liquid and semi-solid matrices. These results provide some of the first estimates of removal efficiencies and inactivation times in realistic environmental conditions for Ascaris on surfaces while supporting the use of OPC mortar mix designs with fly ash in interventions to reduce Ascaris transmission in rural LMIC households. Author SummarySoil-transmitted helminths, like Ascaris, are parasites that are major contributors to disease in children and women of childbearing age in low- and middle-income countries. Interventions, like replacing soil floors in households with cement-based flooring, may reduce exposure to Ascaris eggs which cause infections, but there is little information on how or why these interventions may be effective. This study investigates the effectiveness of simple cleaning methods, like mopping, in removing Ascaris eggs from cement-based surfaces and explores how long these eggs can survive on these surfaces under different environmental conditions. We tested two types of cement-based surfaces, a traditional cement-based mortar mix, and a more sustainable cement-based mortar mix, and found that mopping removed over 92% of Ascaris eggs, with no differences between cement mixes. Experiments simulating wet and dry seasonal conditions showed that Ascaris eggs survive longer in cooler environments, again with no differences between cement mixes. These findings provide important insights into the role of cement-based flooring in interrupting disease transmission and suggest sustainable cement-based mortar mixes are a feasible alternative to traditional cement-based mortar mixes.

microbiology↗

bioRxiv2024

Pathogens and Antimicrobial Resistance Genes in Household Environments: A Study of Soil Floors and Cow Dung in Rural Bangladesh

In low- and middle-income countries, living in homes with soil floors and animal cohabitation may expose children to fecal organisms, increasing risk of enteric and antimicrobial-resistant infections. Our objective was to understand whether cow cohabitation in homes with soil floors in rural Bangladesh contributed to the presence and diversity of potential pathogens and antimicrobial resistance genes (ARGs) in the home. In 10 randomly selected households in rural Sirajganj District, we sampled floor soil and cow dung, which is commonly used as sealant in soil floors. We extracted DNA and performed shotgun metagenomic sequencing to explore potential pathogens and ARGs in each sample type. We detected 6 potential pathogens in soil only, 49 pathogens in cow dung only, and 167 pathogens in both soil and cow dung. Pathogen species with relative abundances >5% in both soil floors and cow dung from the same households included E. coli (N=8 households), Salmonella enterica (N=6), Klebsiella pneumoniae (N=2), and Pseudomonas aeruginosa (N=1). Cow dung exhibited modestly higher pathogen genus richness compared to soil floors (Wilcoxon signed-rank test p=0.002). Using Bray-Curtis dissimilarity, pathogen species community composition differed between floors and cow dung (PERMANOVA p<0.001). All soil floors and cow dung samples contained ARGs against antibiotic classes including sulfonamides, rifamycin, aminoglycosides, lincosamides, and tetracycline. Paired floor and cow dung samples shared ARGs against rifamycin. Our findings support the development of interventions to reduce soil and animal feces exposure in rural, low-income settings. ImportanceIn low-income countries, inadequate housing materials and animal cohabitation can lead to fecal contamination of rural homes. Contaminated soil floors are difficult to clean and may harbor organisms causing illness and antibiotic resistance, especially in young children, who frequently ingest soil. We sequenced soil floor and cow dung samples from households in Sirajganj district, Bangladesh and identified pathogens and antibiotic resistance genes. We detected 167 pathogens in both soil and cow dung; pathogens present in both sample types at the highest relative abundances were E. coli, Salmonella enterica, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Antibiotic resistance genes were found in all samples. In cow dung, the most common genes conferred resistance to the antibiotics lincosamide, rifamycin, cephamycin, and tetracycline. In soil floors, the most common genes conferred resistance to rifamycin, sulfonamides, and aminoglycosides. Household soil and cow dung may be important reservoirs of pathogens and antimicrobial resistance in low-income countries.

microbiology↗

bioRxiv2024

Evaluating the Survival and Removal of Escherichia coli from Surfaces Made with Traditional and Sustainable Cement-Based Materials in Field-Relevant Conditions

Soil household floors are common in low- and middle-income countries (LMICs) and can serve as reservoirs of enteric pathogens. Cement-based floors may interrupt pathogen transmission, but little is known about pathogen survival or removal from cement-based surfaces. This study investigated the survival of Escherichia coli (E. coli), an indicator of fecal contamination, on cement-based surfaces and evaluated its reduction through common household activities (mopping, sweeping, and walking). We compared E. coli fate on three mixes: 1) Ordinary Portland Cement (OPC) concrete (used in the United States), 2) OPC mortar (used in Bangladesh), and 3) OPC mortar with fly ash (a sustainable alternative to the Bangladesh mix). Additionally, we compared outcomes on cement-based surfaces with and without soil and at two temperatures representing the dry and wet seasons in Bangladesh. After 4 hours on the cement-based surfaces, E. coli decayed more than 1.1 log10(C/Co) under all conditions tested, which is significantly faster than in bulk soils. The higher temperature increased the decay rate constant (p = 5.56*10-8) while soil presence decreased it (p = 2.80*10-6). Sweeping and mopping resulted in high levels of removal for all mixes, with a mean removal of 71% and 78%, respectively, versus 22% for walking. The concrete and mortar mix designs did not impact E. coli survival or removal (p > 0.20). Cement-based floors made with a fly ash mix performed similarly to traditional cement-based floors, supporting its potential use as a more sustainable intervention to reduce fecal contamination in rural LMIC household settings. ImportanceCement-based surfaces may serve as a health intervention to reduce the fecal-oral transmission of pathogens in household settings, but there is a critical lack of evidence about the fate of indicator organisms on these surfaces, especially in field-relevant conditions. This study provides some of the first insights into E. coli survival on cement-based surfaces and the effectiveness of daily activities for removing E. coli. Additionally, this study explores the fate of E. coli on cement-based surfaces made with fly ash (which contributes fewer CO2 emissions) versus traditional cement mixes. We found that E. coli had similar survival and removal across all mix designs, demonstrating that fly ash mixes are feasible for use in household settings (e.g., in floors). The findings enhance understanding of fecal-oral transmission pathways and support the use of fly ash mixes in cement-based flooring in future epidemiologic studies assessing effects on enteric disease burdens.

microbiology↗

bioRxiv2024

Social Isolation During Adolescence Differentially Affects Spatial Learning in Adult Male and Female Mice

Social isolation is a risk factor for cognitive impairment. Adolescents may be particularly vulnerable to these effects, because they are in a critical period of development marked by significant physical, hormonal, and social changes. However, it is unclear if the effects of social isolation on learning and memory are similar in both sexes or if they persist into adulthood after a period of recovery. We socially isolated male and female 129Sv/Ev mice throughout adolescence (post-natal days 29-56), provided a 2-week re-socialization recovery period, and then tested spatial learning and cognitive flexibility in the active place avoidance task. After behavioral testing, mice were injected with 5-bromo-2-deoxyuridine (BrdU) so that lasting effects of social isolation on cell proliferation in the dentate gyrus could be examined. We found that in males, isolation led to a modest impairment in the rate of initial spatial learning, whereas in females, initial learning was unaffected. However, when the location of the shock zone was switched during the conflict variant of the task, cognitive flexibility was impaired in females only. Similarly, social isolation reduced cell proliferation in the ventral dentate gyrus only in females. Together, these findings indicate that social isolation during adolescence differentially impairs spatial processing in males and females, with effects that persist into adulthood.

neuroscience↗

bioRxiv2024

A draft Arab pangenome reference

Pangenomes represent a significant shift from relying on a single reference sequence to a robust set of assemblies, Arab populations remain significantly underrepresented; hence, we present the first Arab Pangenome Reference (APR) utilizing 53 individuals of diverse Arab ethnicities. We assembled nuclear and mitochondrial pangenomes using 35.27X high-fidelity long reads, 54.22X ultralong reads and 65.46X Hi-C reads yielded contiguous haplotype-phased de novo assemblies of exceptional quality, with an average N50 of 124.28 Mb. We discovered 111.96 million base pairs of novel euchromatic sequences absent from existing human pangenomes, the T2T-CHM13, GRCh38 reference human genomes, and other public datasets. We identified 8.94 million population-specific small variants and 235,195 structural variants within the Arab pangenome. We detected 883 gene duplications including 15.06% associated with recessive diseases and 1,436 bp of novel mitochondrial pangenome sequence. Our study provides a valuable resource for future genomic medicine initiatives in Arab population and other global populations.

genomics↗

bioRxiv2024

Chronic Social Defeat Stress Gives Rise to Social Avoidance Through Fear Learning

Chronic social defeat stress (CSDS), a widely used rodent model of stress, reliably leads to decreased social interaction in stress susceptible animals. Here, we investigate a role for fear learning in this response using 129Sv/Ev mice, a strain that is more vulnerable to CSDS than the commonly used C57BL/6 strain. We first demonstrate that defeated 129Sv/Ev mice avoid a CD-1 mouse, but not a conspecific, indicating that motivation to socialize is intact in this strain. CD-1 avoidance is characterized by approach behavior that results in running in the opposite direction, activity that is consistent with a threat response. We next test whether CD-1 avoidance is subject to the same behavioral changes found in traditional models of Pavlovian fear conditioning. We find that associative learning occurs across 10 days CSDS, with defeated mice learning to associate the color of the CD-1 coat with threat. This leads to the gradual acquisition of avoidance behavior, a conditioned response that can be extinguished with 7 days of repeated social interaction testing (5 tests/day). Pairing a CD-1 with a tone leads to second-order conditioning, resulting in avoidance of an enclosure without a social target. Finally, we show that social interaction with a conspecific is a highly variable response in defeated mice that may reflect individual differences in generalization of fear to other social targets. Our data indicate that fear conditioning to a social target is a key component of CSDS, implicating the involvement of fear circuits in social avoidance.

animal behavior and cognition↗